Alcohol and drug addiction has been blamed for a 5.5pc rise in babies taken into care.
The figure was revealed in a report monitoring HSE activities between January and November last year.
The increase was attributed to several factors, including a rise in babies born to alcohol or drug addicts. In addition, the economic downturn resulted in unemployment and led to additional stress on already vulnerable families.
There was also an increase in the reporting of cases following better public awareness of child protection and welfare issues.
The report revealed that there has been a slight reduction in the number of foster carers with an allocated social worker.
This is despite the legal right of every child in care to have a social worker allocated to them.
As a result, more than 20pc of children in care now have no allocated social worker.
The HSE has previously argued that the rising number of children being taken into care reflected the nation's changing demographics, with more children in the general population.
In 2002, the number of children in care was 4,921.
The figure had risen to 5,336 at the end of 2006 and 5,477 by June the following year.
The HSE said at the time that there was a "gradual upward trend in the figures which is going to represent the changes in demographics and the bigger numbers of children in the population".
Norah Gibbons, director of advocacy for children's charity Barnados, said the shortage of social workers was of major concern. She said a social worker was a basic requirement for planning care.
Ms Gibbons insisted children should not be in care just because their family is poor, calling for better family support services to prevent this.
She said parents who are drug addicts are often only capable of focusing on their next fix, rather than their child's welfare.
Figures show almost €90m a year is spent to keep about 400 children in residential care, at an average cost of €4,294 per child per week.
In addition, a small number of children are sent overseas for treatment at an average cost to the taxpayer of €4,692 per child per week.
Placing children in foster care is far more cost-effective than using residential care homes.
Foster carers receive a weekly payment of €325 per child under 12 years of age and €352 for those over 12.
The bulk of the 5,676 children in care at the end of July 2009 were in foster care.